Lazydock

2025-02-06 16:08:21

Focus on
1. fix bugs in lazydock/scripts/prepare_gmx.py, run_gmx.py, ana_gmx.py


What's New
- addon: lazydock\pml_plugin\_init_.py: add RRCS calculation and shader application features
- addon: lazydock\web\dinc.py: add DINC ensemble docking functionality
- addon: lazydock\scripts\dock.py: add DINC-Ensemble docking command tool
- addon: lazydock\scripts\dock.py: add cluster_result: add cluster analysis for docking results
- addon: add lazydock/scripts/md_task.py: add optimized CLI tools for MD-TASK
- addon: lazydock/scripts/md_task.py: add contact map analysis for MD-TASK
- addon: lazydock/gmx/mda/convert.py: add PDB string converter


Minor Addon
- minor-addon: lazydock\scripts\ana_interaction.py: simple_analysis: add reference residue analysis
- minor-addon: lazydock\scripts\dock.py: vina: add customization options for config file name and Vina arguments
- minor-addon: lazydock\scripts\run_gmx.py: simple_protein: add em-args to run_gmx.py
- minor-addon: lazydock\pml\autodock_utils.py: DlgFile: add max_iter parameter to rmsd_cluster method
- minor-addon: lazydock\scripts\run_gmx.py: simple-protein: add start time argument and sleep until start
- minor-addon: lazydock\scripts\prepare_gmx.py: add C-terminal option and modify N-terminal logic
- minor-addon: lazydock\scripts\ana_gmx.py: simple: add customizable group and xmax options for analysis
- minor-addon: lazydock\scripts\prepare_gmx.py: protein: support multiple chains in protein
- minor-addon: lazydock\scripts\run_gmx.py: add check for existing md.tpr file
- minor-addon: lazydock/scripts/ana_gmx.py: simple: add -ns option to xvg_compare and xvg_show
- minor-addon: lazydock/scripts/run_gmx.py: simple_protein: add maxwarn option to grompp commands
- minor-addon: lazydock/scripts/ana_gmx.py: simple: add free energy landscape analysis by md-davis


BUG-FIX
- fix-bug: scripts/ana_interaction.py: pass ref_res to calc_interaction_from_dlg, add reference residues sorting and formatting
- fix-bug: My_Progs/LazyDock/lazydock/web/dinc.py: run_dock_on_DINC_ensemble: fix waiting logic and result file extraction process
- fix-bug: lazydock\scripts\ana_gmx.py: simple: correct SASA calculation in Gromacs
- fix-bug: lazydock\scripts\ana_gmx.py: simple: add -c 1 option to dit xvg_compare for consistency
- fix-bug: lazydock\scripts\run_gmx.py: simple-protein: optimize start time functionality
- fix-bug: lazydock\gmx\thirdparty\cgenff_charmm2gmx.py: use only file names for prm and itp inclusions for fit run_gmx: simple_complex: equilibration: STEP 2
- fix-bug: lazydock\web\cgenff.py: get_result_from_CGenFF: correct function name and update LastEditTime
- fix-bug: lazydock\scripts\prepare_gmx.py: ligand: prepare_ligand: improve ff-dir handling logic to avoid not copy abs ff-dir
- fix-bug: lazydock\scripts\run_gmx.py: update prompt matching
- fix-bug: lazydock\scripts\prepare_gmx.py: complex:prepare_complex_topol: add newline at the end of topol file in prepare_gmx.py
- fix-bug: lazydock\scripts\run_gmx.py: add genion_groups argument and adjust related functionality
- fix-bug: lazydock\scripts\prepare_gmx.py: ligand: fix_name_in_mol2: update mol2 file parsing
- fix-bug: lazydock\scripts\ana_gmx.py: simple: gyrate: remove parameter from gyrate function for compatibility
- fix-bug: lazydock/scripts/run_gmx.py: simple_protein: main_process: add continue statement for md.tpr check in simple_protein command
- fix-bug: lazydock/gmx/run.py: Gromacs: run_command_with_expect: add quotes around bash_path in expect script to avoid path parsing issues
- fix-bug: lazydock/scripts/_script_utils_.py: excute_command: update to mbapy 870aaf003c380a1172ca4bb84c676a1c32bcce27


CODE-FIX
- fix-code: lazydock/pml/ligplus_interaction.py: improve path handling in ligplus_interaction
- fix-code: lazydock\pml\align_to_axis.py: change dss option to be False in default, avoiding ss change
- fix(scripts): correct SASA and covar analysis in ana_gmx.py
- fix-code: lazydock\scripts\ana_gmx.py: simple: enhance data visualization and analysis
- fix-code: lazydock\scripts\run_gmx.py: simple-protein: make mdp file arguments required and improve missing file warning
- fix-code: lazydock\scripts\ana_gmx.py: simple: modify RMSF and covariance analysis in Gromacs script
- fix-code: lazydock\scripts\prepare_gmx.py: ligand: avoid using pymol to disorder the lig_ini.pdb lines; add copy for topol.top
- fix-code: lazydock\scripts\run_gmx.py: simple_ligand: add group selection for energy analysis and improve ligand handling
- fix-code: My_Progs/LazyDock/lazydock/web/dinc.py: run_dock_on_DINC_ensemble: improve DINC browser automation with logging and screenshot
- fix-code: lazydock\web\cgenff.py: get_result_from_CGenFF: improve CGenFF result generation and download process
- fix-code: lazydock\scripts\prepare_gmx.py: ligand: prepare_ligand: handle CGenFF download failure and improve error logging
- fix-code: lazydock\scripts\prepare_gmx.py: refactor force field directory handling
- fix-code: lazydock/scripts/prepare_gmx.py: protein: improve handling of termini for multi-chain proteins in prepare_gmx.py
- fix-code: lazydock/scripts/run_gmx.py: simple_protein: update visualization commands
- fix-code: lazydock/gmx/run.py: update expect script timeout setting
- fix-code: lazydock/scripts/ana_gmx.py: simple: add timeout handling for Gromacs commands to fit different Gromacs versions
- fix-code: lazydock/scripts/md_task.py: network: add more info in argument parser
- fix-code: lazydock/scripts/md_task.py: fix import


Remove
None or a little.


Other Changes
- fix-code: requirements.json: add compas as an optional dependency
- build: add lazydock_md_task as a new dependency
- build(requirements): add md-davis package
- build: add plip as a new dependency
- build: update mbapy dependency to version 0.11.0

2024-12-18 21:18:57

Focus on
1. add Gromacs scripts
2. add scripts and fix bug in docs


What's New
- addon: lazydock\scripts\eval_modeling.py: add eval_modeling script for protein modeling evaluation
- addon: lazydock\gmx\thirdparty\cgenff_charmm2gmx.py: Add new script `cgenff_charmm2gmx.py` to convert CHARMM parameters to GROMACS format, with compatibility with Networkx 3.X. THIS SCRIPT IS FROM https://github.com/Lemkul-Lab/cgenff_charmm2gmx
- addon: lazydock\storage\lazydock-cli-scripts-list.json: add gmx script
- addon: add lazydock\gmx\run.py: add Gromacs class for running GROMACS commands
- addon: lazydock\pml\utils.py: add get_seq function to get protein sequences
- addon: lazydock\scripts\gmx.py: add prepare_complex script for GROMACS


Minor Addon
- minor-addon: lazydock\scripts\dock.py: HDOCK and HPEPDOCK: add GUI option for browser and refactor docking process
- minor-addon: lazydock_pymol_plugin\__init__.py: add align_pose_to_axis command to LazyDock Pymol Plugin
- minor-addon: lazydock\pml\align_to_axis.py: add 'alter' method to align pose to axis
- minor-addon: lazydock\pml\align_to_axis.py: add dss option to align_pose_to_axis function


BUG-FIX
- fix-bug: lazydock\pml\align_to_axis.py: sort_vertices: improve bounding box alignment algorithm
- fix-bug: lazydock\gmx\thirdparty\__init__.py: create thirdparty init file
-


CODE-FIX
- fix-code: lazydock\scripts\eval_modeling.py: add QMEAN and QMEANDisCo support and improve result formatting
- fix-code: lazydock\scripts\dock.py: update run_vina task to include vina_name argument
-


Remove
None or a little.


Other Changes
- build(dependencies): add networkx
- requirements.json: remove compas because it require numpy<2

2024-12-10 11:25:58

Focus on
1. add scripts (get_pocket, ana_interaction, dock)
2. fix-bugs in interaction analysis functionality


What's New
- addon: lazydock\scripts\get_pocket.py
- addon: add get_pocket and ana_interaction
- addon: lazydock\pml\autodock_utils.py: implement DLG file merging functionality
- addon: lazydock\scripts\ana_interaction.py: add simple analysis script for docking results
- addon: lazydock\scripts\dock.py: add dock script for molecular docking
- addon: lazydock\scripts\dock.py: add convert-result command for docking result conversion
- addon: add lazydock\web\lig_eval.py: add get_score_from_SwissADME and get_score_from_SwissTargetPrediction
- addon: add lazydock\web\hdock.py: add HDOCK docking functionality
- addon: lazydock\scripts\dock.py: add HDOCK docking support
- addon: lazydock\web\hdock.py: add support for HPEPDOCK docking
- addon: lazydock\scripts\dock.py: add HPEPDOCK docking command-line tool


Minor Addon
- minor-addon: lazydock\web\gen_pocket.py: make ligand_path parameter optional in get_pocket_box_from_ProteinPlus function
- minor-addon: lazydock\pml\ligplus_interaction.py: add force_cwd option to make sure the cwd works in Windows
- minor-addon: lazydock\pml\ligplus_interaction.py: add w_dir option
- addon: lazydock\pml\interaction_utils.py: add hydrogen_atom_only option
- addon: lazydock\scripts\ana_interaction.py: add hydrogen_atom_only option
- minor-addon: lazydock\scripts\ana_interaction.py: simple_analysis: output_fromater_receptor: sort interactions by residue number and improve output formatting
- minor-addon: lazydock\scripts\dock.py: hdock: support docking with receptor and ligand files directly


BUG-FIX
- fix-bug: lazydock\pml\plip_interaction.py: calcu_receptor_poses_interaction: avoid merge error when taskpool is None
- fix-bug: lazydock\scripts\get_pocket.py: improve pocket detection and output organization
- fix-bug: lazydock/scripts/dock.py: hdock: run_hdock_web: make right w_dir parsing when config_path is tuple
- fix-bug: lazydock\scripts\dock.py: hpepdock: update argument parser by change attributes
- fix-bug: lazydock\scripts\dock.py: add result_prefix argument to hdock_run_fn_warpper to specify the HDOCK and HPEPDOCK


CODE-FIX
- fix-code: lazydock\pml\ligplus_interaction.py: replace ValueError with put_err for better error handling
- fix-code: lazydock\pml\plip_interaction.py: handle unsupported mode and PLIP analysis errors
- fix-code: lazydock\pml\autodock_utils.py: update PDB pattern to match more case
- fix-code: lazydock\web\lig_eval.py: rename lig_eval.py output files with prefix
- fix-code: lazydock\web\lig_eval.py: handle "too large" error for lig_SMILES in SwissADME and SwissTargetPrediction
- fix-code: lazydock\scripts\dock.py: vina: change config file handling to directory-based
- fix-code: lazydock\web\hdock.py: add page refresh for HDOCK and HPEPDOCK result checking


Remove
None or a little.


Other Changes
- build(dependencies): update mbapy to version 0.10.2
- Upgrade mbapy from version 0.10.0 to 0.10.2 in requirements.json

2024-11-06 22:06:27

2024-11-06 22:06:27


Focus on
1. fix interaction functionality's code to make pymol, PLIP and LigPlus as ONE.
2. add RMSD functionality to pymol-plugin.


What's New
- addon: setup.py: add entry point for lazydock_pymol_plugin.main:exec_from_cli in setup.py.
- addon: lazydock_pymol_plugin\main.py: Add exec_from_cli function to GUILauncher for command line interface execution.
- addon: lazydock_pymol_plugin\main.py: add LazyPml page and uni_load button
- add: lazydock_pymol_plugin\_nicegui\local_file_picker.py
- add: lazydock_pymol_plugin\lazy_pml.py
- addon: add lazydock\pml\ligplus_interaction.py
- addon: add lazydock\config.py
- minor-addon: lazydock\pml\interaction_utils.py: add string mode
- addon: lazydock\pml\autodock_utils.py: DlgFile: add method get_top_k_pose
- addon: lazydock_pymol_plugin\lazy_dlg.py: add RMSD functionality


Minor Addon
- minor-addon: lazydock_pymol_plugin\lazy_dlg.py: LazyPose: load_dlg_file: add path parameter
- minor-addon: lazydock\pml\plip_interaction.py: add mode param in string format
- minor-addon: lazydock_pymol_plugin\main.py: add upload for aonther uni-load
- minor-addon: lazydock_pymol_plugin\main.py: GUILauncher: add a taskpool in threads mode tab_panel style fix


BUG-FIX
- fix-bug: lazydock\pml\plip_interaction.py: calcu_receptor_poses_interaction: fix parameter passing for merge_interaction_df


CODE-FIX
- fix-code: lazydock\pml\ligplus_interaction.py: Fix comment clarification in ligplus interaction function.
- fix-code: lazydock\pml\interaction_utils.py: add a string mode 'all'
- fx-code: lazydock_pymol_plugin\lazy_dlg.py: InteractionPage: change mode from int for pymol to string for all methods


Remove
None or a little.


Other Changes
- Add "openbabel-wheel" to requirements.

**Full Changelog**: https://github.com/BHM-Bob/LazyDock/compare/v0.5.0...v0.6.0

2024-10-31 16:54:37


Focus on
1. add pocket utils
2. add RRCS calculation
3. add RMSD calculation for AutoDock result


What's New
- addon: add lazydock\web\gen_pocket.py
- addon: add lazydock\pml\thirdparty\__init__.py
- addon: add lazydock\pml\thirdparty\draw_bounding_box.py
- addon: add lazydock/pml/plip_interaction.py
- addon: lazydock_pymol_plugin\lazy_dlg.py: LazyDLG: add ResultPage
- addon: lazydock\pml\autodock_utils.py: add calcu_RMSD
- addon: lazydock\pyrt\relax.py: add RelaxPDBChain
- addon: lazydock\pyrt\energy_utils.py: add calcu_interface_energy
- addon: lazydock\pml\autodock_utils.py: add calcu_rmsd_by_coords and rmsd_cluster functionality


Minor Addon
- minor-addon: lazydock\web\gen_pocket.py: parse_pocket_box_from_ProteinPlus: add method: mean
- minor-addon: lazydock/pml/autodock_utils.py: ADModel: add default_chain option
- minor-addon: lazydock_pymol_plugin/lazy_dlg.py: InteractionPage: add PLIP calculate
- minor-addon: lazydock\pml\rrcs.py: add _cmd arg
- minor-addon: lazydock\pml\autodock_utils.py: ADModel: add run_idx attribute
- minor-addon: lazydock\pml\autodock_utils.py: DlgFile: rmsd


BUG-FIX
- fix-bug: lazydock_pymol_plugin\lazy_dlg.py: LazyPose: ui_update_ui: remove update for missing self.ui_dlg
- fix-bug: lazydock/pml/plip_interaction.py: get_atom_level_interactions: check receptor and ligand chain


CODE-FIX
- fix-code: lazydock\pml\interaction_utils.py: move sort function to module level for better accessibility
Moved the `sort_func` from within `calcu_receptor_poses_interaction` to the module level
Added type annotations to the `sort_func` for improved code clarity
Updated the `sort_func` to return a list of tuples with str, int, and str types
- fix-code: lazydock\web\gen_pocket.py: get_pocket_box_from_ProteinPlus: specify download path
- fix-code: lazydock\web\gen_pocket.py: add docs-string
- fix-code: setup.py: add lazydock_pymol_plugin as package
- fix-code: lazydock_pymol_plugin\lazy_dlg.py: remove RMSD because too slow


Remove
None or a little.


Other Changes
- use mbapy_lite instead of mbapy
- fix-code: requirements.json: Update mbapy version in requirements.json from 0.7.9 to 0.10.0.

**Full Changelog**: https://github.com/BHM-Bob/LazyDock/compare/v0.4.0...v0.5.0